Uncovering novel epigenetic traits in grapevine resistance against downy and powdery mildew – A multi-omics approach

Abstract

As one of the most important crop plants in the world, securing grapevine yields and production quality is a top priority. This, however, needs to be reconciled with a move towards greater sustainability, which may prove to be an issue due to the extensive use of phytopharmaceuticals in viticulture to fend off against common diseases1. Epigenetics may prove to be extremely useful in the search of the immunity mechanisms of grapevine, due to the prolific and ubiquitous roles. From being one of the key players in orchestrating transcriptional reprogramming to possibly being implicated in immune memory, it is a currently understudied component of grapevine immune responses with tremendous potential2. While studying the epigenome can be elucidative, integrating it with other omics, namely transcriptomics and small RNA(sRNA)-seq only serves to strengthen analysis and future discovery of molecular resistance traits3. This is the mission of the Horizon2020 SHIELD4GRAPE project, starting with multi-omics analysis of grapevine responses and culminating with the development of integrated pest management strategies, promoting viticulture sustainability.

In this work, we performed an infection assay with Plasmopara viticola and Erysiphe necator, causal agents of downy and powdery mildew, using seven minority cultivars from Portugal, Spain, Italy, and Greece, and ‘Chardonnay’ as a susceptible control. We then perform whole-genome bisulfite sequencing, RNA-seq and sRNA-seq, and perform multi-omics integration. By comparing the responses of the tolerant genotypes to infection against ‘Chardonnay’, we uncovered epigenetically-regulated genes, DNAmethylation-sRNAcrosstalk and microRNA(miRNA)-mediated gene silencing. From this Big Data approach, we can elect new resistance marks linked to DNAmethylation or small RNAs, as well as elucidate fundamental mechanisms of epigenetic regulation in this valuable crop plant. Future work is being developed to integrate proteomics and metabolomics data, other scopes of analysis within SHIELD4GRAPE, and capture the complete picture of grapevine immune responses.

References

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Kundu, B. K. & Tanti, B. Decoding plant physiology through systems biology: Integrative multi-omics and computational perspectives for next-generation crop design. Plant Commun. 101668 (2025) doi:10.1016/j.xplc.2025.101668.

Acknowledgements

This work was supported by the European Commission in the frame of the Horizon Europe program, project ‘Shield4Grape’ (grant agreement number 101135088). Views and opinions expressed are those of the authors only and do not necessarily reflect those of the European Union. Neither the European Union nor the granting authority can be held responsible for them. JPP was supported by a FCT PhD Studentship (reference 2024.00649.BD).